Does PlotHiC be available for non-AutoHiC result now?

[wu116]

Thanks for such a nice tools!

But I encountered difficulties in using plothic with HiC-Pro result. I generated a .hic file with hicpro2juicebox.sh a while ago and tried to re-plot HiC heatmap with PlotHiC command like:
plothic -hic sample1.allValidPairs.hic -chr ../chr.sizes -r 100000

This threw out an error:

File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/plothic/ParseHiC.py", line 25, in parse_hic
    hic_max_len = chr_info["assembly"]
KeyError: 'assembly'

I've checked the chr_info and it only contained "ALL" and the other chromosome IDs:

{'ALL': 630988, 'OMOSOME1': 19002562, 'OMOSOME2': 18725070, ...... ,'OMOSOME39': 19189786, 'OMOSOME40': 19427610}

So I modified all the 'assembly' to 'ALL'.

PlotHiC/src/plothic/ParseHiC.py

Lines 25 to 31 in ca34e3d

	hic_max_len = chr_info["assembly"]
	matrix_end = hic_max_len if matrix_end is None else matrix_end
	# logger.info(f"HiC data assembly chromosome length: {hic_max_len}")
	res_max_len = resolution * 1400
	matrix_obj = hic_obj.getMatrixZoomData('assembly', 'assembly', data_type, normalization, "BP", resolution)

This time hicstraw threw out: Error finding block data
So i changed 'ALL' to 'OMOSOME1' and 'OMOSOME40' in line 31 for test but still get new error:

Traceback (most recent call last):
  File "/home/A/miniconda3/envs/plothic/bin/plothic", line 8, in <module>
    sys.exit(main())
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/plothic/cli.py", line 35, in main
    plot_hic(args.hic_file, chr_txt=args.chr_txt, output=args.output, resolution=args.resolution,
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/plothic/PlotHiC.py", line 61, in plot_hic
    plot_matrix(matrix, chr_info=chr_info_sorted, outfile=output, genome_name=genome_name, fig_size=fig_size, dpi=dpi,
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/plothic/PlotMTX.py", line 29, in plot_matrix
    fig, ax = plt.subplots(1, 1, figsize=fig_size, dpi=dpi)
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/matplotlib/pyplot.py", line 1775, in subplots
    fig = figure(**fig_kw)
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/matplotlib/pyplot.py", line 1042, in figure
    manager = new_figure_manager(
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/matplotlib/pyplot.py", line 552, in new_figure_manager
    return _get_backend_mod().new_figure_manager(*args, **kwargs)
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 3500, in new_figure_manager
    fig = fig_cls(*args, **kwargs)
  File "/home/A/miniconda3/envs/plothic/lib/python3.10/site-packages/matplotlib/figure.py", line 2626, in __init__
    self.bbox_inches = Bbox.from_bounds(0, 0, *figsize)

Could you help me to figure it out? Thank!

[Jwindler]

Currently PlotHiC is used for visualization after genome scaffolding. The data format you mentioned will be supported later. If possible, could you send me the file for testing?